Of mammoths, microbes and molecules, paleometagenomes from the past

大量令人信服的证据表明，行星气候系统正在朝着过去12万年来前所未有的状态发展。这些变暖趋势对“整个生态系统”(即微生物、动物群、花卉和昆虫)多样性的影响尚不清楚。检验这一点的一种方法是回顾过去。大约11,000年前，超过100种大型哺乳动物和鸟类在北美灭绝。尽管这些损失的确切原因尚不清楚，但考虑到我们快速变暖的北极，它们潜在的后果在今天仍然格外重要。在北方迅速变暖的情况下，生物群将如何应对？解决这个问题的一种方法是评估他们过去对之前的气候粪便的反应，那些同样或更剧烈的粪便。利用从化石遗骸(哺乳动物和微生物)中收集的遗传特征，我们将调查种群如何对过去类似的气候变化做出反应，并利用这些信息帮助我们为即将到来的损失做好准备。有了这些数据，我们就可以开始解决这样的问题：为什么有些物种灭绝了(猛犸象、乳齿象、树懒、马)，而另一些物种却存活了下来(野牛、熊)？虽然许多人认为气候是造成这些损失的直接原因，但也有人认为，人类(大型猎物)在它们最终的灭亡中发挥了关键作用。也许有效的种群规模是冰川后的很小的时间段，以至于它们实际上处于一个临界点，人类造成了最后的打击。*要理清这两个看似不同的假说，一种方法是研究极端气候变化时期所需动物(猛犸象)的遗传学，当时人类在最后一次冰川和间冰期缺席，大约115-130基尔BP，最近一次22基尔斯BP和更新世/全新世过渡，它们最终在大约11,000年前灭绝。*考虑到我们非凡的冰冻遗产，即加拿大北部的永久冻土，这项工作是可能的。其中包括远古时期的宏观化石组合和花粉记录，但它们基因组的退化残骸。使用最先进的基于捕获(浓缩)的方法，其中一些开发的方法，如果我们的实验室，再加上高通量测序(HTS)，我们现在可以合理的成本和创纪录的时间重建线粒体和整个非重复核基因组。*以下NSERC建议寻求在我们研究优势的基础上，通过准确重建随时间推移的种群大小，并使用基于元基因组捕获的新方法，更好地了解微生物群落通过古代环境DNA(ADNA)对气候变化的生态系统水平的响应，从而解决更新世-全新世灭绝的DNA恢复问题的方法学改进。根据目前的估计轨迹，这些数据将被用来帮助预测未来的生态系统反应。

Abundant and compelling evidence indicates that the planetary climate system is moving toward states not equalled in the last 120,000 years. The implications of these warming trends on `whole-ecosystem' (i.e microbial, faunal, floral and insect) diversity remain unknown. One way to test this is to look back in time. Approximately 11,000 years ago more than 100 species of large mammals and birds went extinct in North America. While the precise causes of these losses remains unclear their underlying consequences remain exceptionally pertinent today, given our rapidly warming artic. How will biota respond given the rapidly warming north? One way to address this is to evaluate how they responded in the past, to prior climatic shits, ones that were equally or more drastic. Using genetic signatures gleaned from fossil remains, (both mammalian and microbial) we will investigate how populations responded to similar climatic shifts in the past and use this information to help prepare us for looming losses in the near future. With these data we can begin to address questions such as why was it that some went extinct (mammoth, mastodons, sloths, horses) while others persisted (bison, bears)? While many argue that climate was the direct cause of these losses, others have suggested that humans (big game hunters) played a critical role in their final demise. Perhaps effective population sizes were so small post glacial time periods that they were effectively at a `tipping point', and that humans dealt the final blow.***One way to disentangle these two, seemingly disparate hypotheses, is to study the genetics of the requisite fauna (mammoths) during times of extreme climate change when humans were absent, during the last glacial and interglacial, some 115-130Kyrs BP and present at the most recent one 22Kyrs BP and the Pleistocene/Holocene transition, where they ultimately went extinct some 11,000 years ago.***This work is possible given our remarkable frozen heritage, i.e. the permafrost of the Canadian north, which contains the macro fossil assemblages and pollen records of deep time, but the degraded remains of their genomes. Using state-of-the-art capture (enrichment) based methods, some developed if our labs, coupled with High-Throughput Sequencing (HTS), we can now rebuild mitochondrial and entire non-repetitive nuclear genomes at reasonable costs and in record time. ***The following NSERC proposal seeks to build upon our research strengths and focus on methodological improvements for aDNA recovery disentangling Pleistocene-Holocene extinctions using accurate reconstructions of population sizes through time, and use novel metagenomic capture-based approaches to better understand ecosystem-level responses of microbial communities to climatic shifts through ancient environmental DNAs (aDNA). These data will be used to help predict future ecosystem responses given current estimated trajectories.